"The team management has confirmed he has torn his hamstring muscle during the second test. But they have to still decide if he returns home," Ehsan Malik, communications director, told Reuters.
Akhtar played his first test in 11 months at Port Elizabeth last week and took four wickets in South Africa's first innings, but the injury prevented him from bowling in the second innings.
Malik also said a disciplinary hearing would be held after television cameras captured Shoaib in an altercation with coach Bob Woolmer in the dressing room before the start of play on the second day on Saturday.
Selectors would decide if any replacements would be send to South Africa, he added.